If you download Crystal Core from CVS then the file 'configure' is included with that. So you have that file unless something was wrong when doing the cvs checkout. It seems you only downloaded the data files for Crystal Core but you forgot to check out the source. See this entry on the url you mention:

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Finally you must get Crystal Core itself. Crystal Core is located in the same repository as Crystal Space. Just check out the 'crystalcore' module.